C-banded karyotypes and polymorphisms in hexaploid oat accessions (Avena spp.) using Wright's stain.

A chromosome C-banding protocol using Wright's stain was employed to compare chromosomes in cultivars and wild accessions of several hexaploid oat taxa (Avena spp.). This technique permits the identification of each of the 21 somatic hexaploid oat chromosomes. Digital images of C-banded cells were captured on computer and used to construct karyotypes of several oat accessions. Polymorphisms for C-bands among oat cultivars and wild accessions are described. These banding polymorphisms can be used to trace introgression of chromosomes from wild sources and to provide physical markers on the genetic map for oat. Although C-banding permits the identification of likely C-genome chromosomes based on comparisons with C-banding patterns in diploid and tetraploid Avena species, the A and D genomes cannot be readily differentiated based on their banding patterns.     

A first-generation microsatellite-based integrated genetic and cytogenetic map for the European rabbit (Oryctolagus cuniculus) and localization of angora and albino

Although the European rabbit (Oryctolagus cuniculus) is used both in agronomics and in research, genomic resources for this species are still limited and no microsatellite-based genetic map has been reported. Our aim was to construct a rabbit genetic map with cytogenetically mapped microsatellites so as to build an integrated genetic and cytogenetic map. A reference population of 187 rabbits comprising eight three-generation families with 10-25 offspring per family was produced. One hundred and ninety-four of 305 previously identified microsatellites were included in this study. Of these, 158 were polymorphic with two to seven alleles. The map reported here comprises 111 markers, including 104 INRA microsatellites, five microsatellites from another source and two phenotypic markers (angora and albino). Ninety markers were integrated into 20 linkage groups. The remaining 21 microsatellites mapped to separate linkage groups, 19 with a precise cytogenetic position and two with only a chromosomal assignment. The genetic map spans 2766.6 cM and covers 20 rabbit chromosomes, excluding chromosomes 20, 21 and X. The density of this map is limited, but we used it to verify the location of angora and albino on chromosomes 15q and 1q, respectively, in agreement with previously published data. This first generation genetic/cytogenetic map will help gene identification and quantitative trait loci mapping projects in rabbit.     

A genetic and cytogenetic map for the duck (Anas platyrhynchos)

A genetic linkage map for the duck (Anas platyrhynchos) was developed within a cross between two extreme Peking duck lines by linkage analysis of 155 polymorphic microsatellite markers, including 84 novel markers reported in this study. A total of 115 microsatellite markers were placed into 19 linkage groups. The sex-averaged map spans 1353.3 cM, with an average interval distance of 15.04 cM. The male map covers 1415 cM, whereas the female map covers only 1387.6 cM. All of the flanking sequences of the 155 polymorphic loci--44 monomorphic loci and a further 41 reported microsatellite loci for duck--were blasted against the chicken genomic sequence, and corresponding orthologs were found for 49. To integrate the genetic and cytogenetic map of the duck genome, 28 BAC clones were screened from a chicken BAC library using the specific PCR primers and localized to duck chromosomes by FISH, respectively. Of 28 BAC clones, 24 were detected definitely on duck chromosomes. Thus, 11 of 19 linkage groups were localized to 10 duck chromosomes. This genetic and cytogenetic map will be helpful for the mapping QTL in duck for breeding applications and for conducting genomic comparisons between chicken and duck.     

The relationship between genetic and cytogenetic maps of pea. I. Standard and translocation karyotypes.

A detailed cytogenetical study of inbred lines of pea and their F1 hybrids has been undertaken to study the relationship between the cytogenetic map and the molecular linkage map. The mitotic karyotypes of a standard pea line, JI15, a translocation line, JI61, and line JI281, a line used in the production of a mapping population, are given. A chromosome rearrangement detected by cytogenetic analysis of mitotic chromosomes has been further defined by synaptonemal complex (SC) analysis and the study of metaphase I chromosome behaviour. This meiotic analysis has allowed a comparison of SC physical lengths, observed chiasma frequencies, and recombination frequencies, as estimated from the genetic map, as a means of comparing physical and genetic distances.     

Expanded genetic map of Gibberella moniliformis (Fusarium verticillioides)

Gibberella moniliformis (Fusarium verticillioides) is primarily a pathogen of maize, but it can also cause disease in other crop species. This pathogenicity, as well as the contamination of food- and feedstuffs with the fumonisin mycotoxins, results in economically significant losses to both farmers and food processors. The dissection of important biological characters in this fungus has been hampered by the lack of a uniformly dense genetic map. The existing restriction fragment length polymorphism-based map contains significant gaps, making it difficult to routinely locate biologically important genes, such as those involved in pathogenicity or mycotoxin production, with precision. We utilized amplified fragment length polymorphisms (AFLPs) to saturate the existing genetic map and added 486 AFLP markers to the approximately 150 markers on the existing map. The resulting map has an average marker interval of 3.9 map units and averages approximately 21 kb/map unit. The additional markers expanded the map from 1,452 to 2,188 map units distributed across 12 chromosomes. The maximum distance between adjacent markers is 29 map units. We identified AFLP markers less than 1 map unit from the mating type (MAT) locus and 2.5 map units from the spore killer (SK) locus; eight AFLP markers map within 8.5 units of the FUM1 (fumonisin biosynthetic) locus. The increased saturation of this map will facilitate further development of G. moniliformis as a model system for the genetic and population genetic studies of related, but less genetically tractable, plant pathogenic fungi.     

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes.

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.     

Sex-specific recombination rates in zebrafish (Danio rerio)

In many organisms, the rate of genetic recombination is not uniform along the length of chromosomes or between sexes. To compare the relative recombination rates during meiosis in male and female zebrafish, we constructed a genetic map based on male meiosis. We developed a meiotic mapping panel of 94 androgenetic haploid embryos that were scored for genetic polymorphisms. The resulting male map was compared to female and sex-average maps. We found that the recombination rate in male meiosis is dramatically suppressed relative to that of female meiosis, especially near the centromere. These findings have practical applications for experimental design. The use of exclusively female meiosis in a positional cloning project maximizes the ratio of genetic map distance to physical distance. Alternatively, the use of exclusively male meiosis to localize a mutation initially to a linkage group or to maintain relationships of linked alleles minimizes recombination, thereby facilitating some types of analysis.     

Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human.

The domestic dog is increasingly being recognized as a useful model for human disease. The aim of this study was to conduct the first detailed whole-genome comparison of human and dog using bidirectional heterologous chromosome painting (reciprocal Zoo-FISH) analysis. We used whole-chromosome paint probes produced from degenerate oligonucleotide-primed PCR amplification of high-resolution bivariate flow-sorted human and dog chromosomes. No fewer than 68 evolutionarily conserved segments were identified between the dog and the human karyotypes. The use of elongated metaphase chromosomes for both species allowed the boundaries of each evolutionarily conserved segment to be determined to subband resolution. The distribution of conserved segments is discussed, as are the applications of these data in refining the current status of the dog genome map.     

Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa)

 A foxtail millet-rice comparative genetic map was constructed using mapped rice RFLP markers and wheat genomic and cDNA clones with known map position in rice. About 74% and 37% of the cDNA and genomic clones, respectively, were transferable to foxtail millet, confirming that conservation at the DNA level is greatest in genic regions. A high degree of conserved colinearity was observed between the two genomes. Five entire foxtail millet chromosomes appear to be colinear with five entire rice chromosomes. The remaining four foxtail millet linkage groups each show colinearity with segments of two rice chromosomes. The rearrangements of rice chromosomes 3 and 10 to form foxtail millet chromosome IX, and 7 and 9 to form chromosome II are very similar to those required to form maize chromosomes 1 and 7 and sorghum linkage groups C and B, indicating Setaria’s clear taxonomic position within the subfamily of the Panicoideae. Received: 18 December 1996 / Accepted: 4 August 1997     

Expanded Genetic Map of Gibberella moniliformis (Fusarium verticillioides)

Gibberella moniliformis (Fusarium verticillioides) is primarily a pathogen of maize, but it can also cause disease in other crop species. This pathogenicity, as well as the contamination of food- and feedstuffs with the fumonisin mycotoxins, results in economically significant losses to both farmers and food processors. The dissection of important biological characters in this fungus has been hampered by the lack of a uniformly dense genetic map. The existing restriction fragment length polymorphism-based map contains significant gaps, making it difficult to routinely locate biologically important genes, such as those involved in pathogenicity or mycotoxin production, with precision. We utilized amplified fragment length polymorphisms (AFLPs) to saturate the existing genetic map and added 486 AFLP markers to the ~150 markers on the existing map. The resulting map has an average marker interval of 3.9 map units and averages ~21 kb/map unit. The additional markers expanded the map from 1,452 to 2,188 map units distributed across 12 chromosomes. The maximum distance between adjacent markers is 29 map units. We identified AFLP markers less than 1 map unit from the mating type (MAT) locus and 2.5 map units from the spore killer (SK) locus; eight AFLP markers map within 8.5 units of the FUM1 (fumonisin biosynthetic) locus. The increased saturation of this map will facilitate further development of G. moniliformis as a model system for the genetic and population genetic studies of related, but less genetically tractable, plant pathogenic fungi.     

Chromosome numbers and karyotypes of Catasetum species (Orchidaceae)

Mitotic chromosomes of 12 species of Catasetum were assessed to contribute with the karyotypic study of the subtribe Catasetinae (Orchidaceae), expanding the knowledge of this group in terms of chromosomes and supporting its taxonomic and evolutionary analysis. The species are maintained in cultivation in the greenhouse of the Department of Plant Biology/IB/UNICAMP and in the “Orquidário Frederico Carlos Hoehne” of the Botanical Garden of São Paulo. Chromosome counts ranged from 2n = 54 to 2n = 108. Karyotypes were prepared for all species studied, in which there was a predominance of metacentric chromosomes and some submetacentric ones. The chromosome size ranged from 0.5 to 4.9 μm, the total chromosome length ranged from 34.7 to 78.7 μm and the asymmetry index TF% ranged from 21.2 to 42.3. The results obtained so far favor the taxonomy of the genus, allowing to distinguish species with very similar external morphology.     

An SSR genetic map of Sorghum bicolor (L.) Moench and its comparison to a published genetic map.

Sorghum bicolor (L.) Moench is an important grain and forage crop grown worldwide. We developed a simple sequence repeat (SSR) linkage map for sorghum using 352 publicly available SSR primer pairs and a population of 277 F2 individuals derived from a cross between the Westland A line and PI 550610. A total of 132 SSR loci appeared polymorphic in the mapping population, and 118 SSRs were mapped to 16 linkage groups. These mapped SSR loci were distributed throughout 10 chromosomes of sorghum, and spanned a distance of 997.5 cM. More important, 38 new SSR loci were added to the sorghum genetic map in this study. The mapping result also showed that chromosomes SBI-01, SBI-02, SBI-05, and SBI-06 each had 1 linkage group; the other 6 chromosomes were composed of 2 linkage groups each. Except for 5 closely linked marker flips and 1 locus (Sb6_34), the marker order of this map was collinear to a published sorghum map, and the genetic distances of common marker intervals were similar, with a difference ratio 相似文献   

A re-assigned American mink (Neovison vison) map optimal for genome-wide studies

Our previously published second generation genetic map for the American mink (Neovison vison) has been used and redesigned in its best for genome-wide studies with maximum of efficiency. A number of 114 selected markers, including 33 newly developed microsatellite markers from the CHORI-231 mink Bacterial Artificial Chromosome (BAC) library, have been genotyped in a two generation population composed of 1200 individuals. The outcome reassigns the position of some markers on the chromosomes and it produces a more reliable map with a convenient distance between markers. A total of 104 markers mapped to 14 linkage groups corresponding to the mink autosomes. Six markers are unlinked and four markers are allocated to the X chromosome by homology but no linkage was detected. The sex-average linkage map spans 1192 centiMorgans (cM) with an average intermarker distance of 11.4 cM and 1648 cM when the ends of the linkage groups and the autosomal unlinked markers are added. Sex-specific genetic linkage maps were also generated. The male sex-specific map had a total length of 1014.6 cM between the linked markers and an average inter-marker interval of 9.7 cM. The female map has a corresponding length of 1378.6 cM and an average inter-marker interval of 13.3 cM. The study is complemented with additional anchorage for most of the chromosomes of the map by BAC in situ hybridization with clones containing microsatellites strategically selected from the various parts of the genome. This map provides an improved tool for genetic mapping and comparative genomics in mink, also useful for the future assembly of the mink genome sequence when this will be taken forward.     

Extending a RFLP-based genetic map of rye using random amplified polymorphic DNA (RAPD) and isozyme markers

RFLP-based genetic map of rye, developed previously using a cross of lines DS2×RXL10 (F₂ generation), was extended with 69 RAPD and 12 isozyme markers. The actual map contains 282 markers dispersed on all seven chromosomes and spans a distance of 1,140 cM. The efficiency of mapping RAPD markers was close to ten loci per 100-screened arbitrary primers. A strong selection of polymorphic, intensive and reproducible fragments was necessary to reveal individual marker loci that could be assigned to rye chromosomes. Newly mapped markers cover a substantial part of the rye genome and constitute a valuable tool suitable for map saturation, marker-aided selection and phenetic studies. A specific nomenclature for the RAPD loci mapped on individual rye chromosomes, which could be helpful in managing of accumulating data, is proposed. Received: 8 May 2000 / Accepted: 17 October 2000     

A molecular genetic linkage map of mouse chromosome 13 anchored by the beige (bg) and satin (sa) loci

A molecular genetic linkage map of mouse chromosome 13 was constructed using cloned DNA markers and interspecific backcross mice from two independent crosses. The map locations of Ctla-3, Dhfr, Fim-1, 4/12, Hexb, Hilda, Inhba, Lamb-1.13, Ral, Rrm2-ps3, and Tcrg were determined with respect to the beige (bg) and satin (sa) loci. The map locations of these genes confirm and extend regions of homology between mouse chromosome 13 and human chromosomes 5 and 7, and identify a region of homology between mouse chromosome 13 and human chromosome 6. The molecular genetic linkage map of chromosome 13 provides a framework for establishing linkage relationships between cloned DNA markers and known mouse mutations and for identifying homologous genes in mice and humans that may be involved in disease processes.     

Chromosome numbers and karyotypes within the Ranunculus alpestris-group (Ranunculaceae)

The Ranunculus alpestris-group comprises six white-flowered species growing in mostly alpine zones of central and southern European mountains. They all are diploid with 2n=16 chromosomes. The common karyotype of the group was established based on 75 metaphases (6–26 metaphases per species). The haploid karyotype consists of four metacentric (chromosomes 1, 3, 6, 7) and four more or less subtelocentric chromosomes (2, 4, 5, 8). This karyotype is similar to that of other white-flowered European Ranunculus species as well as the yellow-flowered R. thora-group. Analysis of karyotypes partly confirms relationships inferred from molecular phylogenies. Species with this karyotype are placed on rather basal branches in existing phylogenies, which may indicate that this karyotype is primitive within the genus Ranunculus.     

A comparison of the fluorescent karyotypes of the chimpanzee (Pan troglodytes) and man

Individual chimpanzee chromosomes have been identified by their characteristic banding revealed by quinacrine fluorescent staining. A fluorescent karyotype of this species was set up to be compared with the standard human fluorescent karyotype. It was found that chromosomes 1, 3, 11, 12, 14 and X-chromosome of the chimpanzee appear to have banding patterns similar to the equivalent human chromosomes. Chromosomes 6, 7, 8, 10 and 13 also had a fluorescent pattern corresponding to the human chromosomes of the same number, particularly in the long arm. Remarkable variation in intensity and/or size of fluorescent regions was frequently found in the short arm of satellited acrocentric chromosomes 13, 14, 15, 22 and 23. Variations occurred between homologues and between individuals. Such variable fluorescence in a specific chromosomal region of an individual animal is a reproducible characteristic. Unlike its human counterpart, the distal segment in the long arm of the chimp's Y-chromosome is not brightly fluorescent. An earlier report is thus confirmed.     

A genetic linkage map of microsatellites in the domestic cat (Felis catus)

Of the nonprimate mammalian species with developing comparative gene maps, the feline gene map (Felis catus, Order Carnivora, 2N = 38) displays the highest level of syntenic conservation with humans, with as few as 10 translocation exchanges discriminating the human and feline genome organization. To extend this model, a genetic linkage map of microsatellite loci in the feline genome has been constructed including 246 autosomal and 7 X-linked loci. Two hundred thirty-five dinucleotide (dC. dA)n. (dG. dT)n and 18 tetranucleotide repeat loci were identified and genotyped in a two-family, 108-member multigeneration interspecies backcross pedigree between the domestic cat (F. catus) and the Asian leopard cat (Prionailurus bengalensis). Two hundred twenty-nine loci were linked to at least one other marker with a lod score >/=3.0, identifying 34 linkage groups. Representative markers from each linkage group were assigned to specific cat chromosomes by somatic cell hybrid analysis, resulting in chromosomal assignments to 16 of the 19 feline chromosomes. Genome coverage spans approximately 2900 cM, and we estimate a genetic length for the sex-averaged map as 3300 cM. The map has an average intragroup intermarker spacing of 11 cM and provides a valuable resource for mapping phenotypic variation in the species and relating it to gene maps of other mammals, including human.     

Relationship between Chromosome 9 of Maize and Wheat Homeologous Group 7 Chromosomes

Comparison of the genetic map of maize chromosome 9 with maps of wheat chromosomes has revealed a high degree of colinearity between maize chromosome 9 and the group 4 and 7 chromosomes of wheat. The order of DNA markers on the short arm and a proximal region of the long arm of the genetic map of maize chromosome 9 is highly conserved with the marker order on the short arm and proximal region of the long arm of the genetic maps of the wheat homeologous group 7 chromosomes. A major part of the long arm of the genetic map of maize chromosome 9 is homeologous with a short segment in the proximal region of the long arm of the genetic map of the wheat group 4 chromosomes. Evidence is also presented that maize chromosome 9 has diverged from the wheat group 7 chromosomes by both a pericentric and a paracentric inversion. The paracentric inversion is probably unique to maize among the major cereal genomes.     

Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones

Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.